6S5V

Crystal structure of the Cap-Midlink region of the H5N1 Influenza A virus polymerase in complex with a Cap-domain binding analogue

External Resource: Annotation

Domain Annotation: ECOD Classification
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A [auth AAAA]	PF20950	e6s5vAAAA1	A: alpha arrays	X: Helical domain in PB2 (From Topology)	H: Helical domain in PB2 (From Topology)	T: Helical domain in PB2	F: PF20950	ECOD (1.6)
A [auth AAAA]	PF00604	e6s5vAAAA2	A: a+b three layers	X: Polymerase basic protein 2 cap-binding domain (From Topology)	H: Polymerase basic protein 2 cap-binding domain (From Topology)	T: Polymerase basic protein 2 cap-binding domain	F: PF00604	ECOD (1.6)
B [auth ABAA]	PF20950	e6s5vABAA2	A: alpha arrays	X: Helical domain in PB2 (From Topology)	H: Helical domain in PB2 (From Topology)	T: Helical domain in PB2	F: PF20950	ECOD (1.6)
B [auth ABAA]	PF00604	e6s5vABAA1	A: a+b three layers	X: Polymerase basic protein 2 cap-binding domain (From Topology)	H: Polymerase basic protein 2 cap-binding domain (From Topology)	T: Polymerase basic protein 2 cap-binding domain	F: PF00604	ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A [auth AAAA], B [auth ABAA]	PF00604	Influenza RNA polymerase PB2 CAP binding domain (Flu_PB2_5th)	Influenza RNA polymerase PB2 CAP binding domain	Influenza virus encodes a large, multidomain RNA-dependent RNA polymerase that can both transcribe and replicate the viral RNA genome. In influenza virus, the polymerase is composed of three polypeptides: PB1, PB2 and PA/P3. PB1 houses the polymerase ...	Influenza virus encodes a large, multidomain RNA-dependent RNA polymerase that can both transcribe and replicate the viral RNA genome. In influenza virus, the polymerase is composed of three polypeptides: PB1, PB2 and PA/P3. PB1 houses the polymerase active site, whereas PB2 and PA/P3 contain, respectively, cap-binding [1] and endonuclease domains required for transcription initiation by cap-snatching [2]. This entry represents the CAP binding domain [2].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A [auth AAAA], B [auth ABAA]	Polymerase basic protein 2	5'-3' RNA polymerase activity catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid RNA polymerase activity transferase activity RNA-dependent RNA polymerase activity nucleotidyltransferase activity catalytic activity transferase activity, transferring phosphorus-containing groups RNA binding binding organic cyclic compound binding nucleic acid binding	symbiont-mediated perturbation of host cellular process biological process involved in interspecies interaction between organisms biological process involved in interaction with host biological process involved in symbiotic interaction symbiont-mediated suppression of host transcription symbiont-mediated suppression of host gene expression symbiont-mediated suppression of host mRNA transcription via inhibition of RNA polymerase II activity modulation by symbiont of host process symbiont-mediated perturbation of host gene expression cellular process symbiont-mediated perturbation of host transcription modulation of process of another organism cellular biosynthetic process cellular metabolic process symbiont-mediated perturbation of host cellular process biological process involved in interspecies interaction between organisms biological process involved in interaction with host biological process involved in symbiotic interaction symbiont-mediated suppression of host transcription symbiont-mediated suppression of host gene expression symbiont-mediated suppression of host mRNA transcription via inhibition of RNA polymerase II activity modulation by symbiont of host process symbiont-mediated perturbation of host gene expression cellular process symbiont-mediated perturbation of host transcription modulation of process of another organism cellular biosynthetic process cellular metabolic process RNA metabolic process viral life cycle primary metabolic process nucleobase-containing compound biosynthetic process macromolecule biosynthetic process nucleic acid metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process nucleic acid biosynthetic process viral genome replication biosynthetic process viral RNA genome replication viral process metabolic process macromolecule metabolic process viral gene expression cap snatching negative stranded viral RNA transcription viral transcription RNA-templated viral transcription 7-methylguanosine mRNA capping 7-methylguanosine RNA capping RNA capping gene expression mRNA processing mRNA metabolic process RNA 5'-end processing RNA processing DNA-templated transcription	host intracellular membrane-bounded organelle host cellular component host intracellular part host cell cytoplasm host cell part host intracellular region cellular anatomical entity host cell mitochondrion host cell cytoplasm part host intracellular organelle host cell nucleus virion component

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A [auth AAAA], B [auth ABAA]	IPR001591	Influenza RNA-dependent RNA polymerase subunit PB2	Family
A [auth AAAA], B [auth ABAA]	IPR049106	Influenza RNA polymerase PB2, N-terminal region	Domain
A [auth AAAA], B [auth ABAA]	IPR049115	Influenza RNA polymerase PB2, C-terminal domain	Domain
A [auth AAAA], B [auth ABAA]	IPR049110	Influenza RNA polymerase PB2, second domain	Domain
A [auth AAAA], B [auth ABAA]	IPR049114	Influenza RNA polymerase PB2, sixth domain	Domain
A [auth AAAA], B [auth ABAA]	IPR049113	Polymerase basic protein 2, helical domain	Domain
A [auth AAAA], B [auth ABAA]	IPR049111	Influenza RNA polymerase PB2, middle domain	Domain
A [auth AAAA], B [auth ABAA]	IPR048298	Influenza RNA polymerase PB2, CAP binding domain	Domain
A [auth AAAA], B [auth ABAA]	IPR037258	PB2, C-terminal	Homologous Superfamily

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.